dCaP: detecting differential binding events in multiple conditions and proteins

BMC Genomics

Table 1 Proportions of TAL1 differential binding in the three categories overlapping with relevant biological features.

	A. binary-only	B. cap-only	C. common
induced genes ¹	18.77%	*** 32.83%	26.20%
repressed genes ¹	9.85%	9.94%	6.89%
all differential expressed genes ¹	28.62%	*** 42.76%	33.09%
non-differential expressed genes ¹	52.08%	49.46%	50.75%
GATA1 binding peaks ²	36.03%	*** 95.68%	63.17%
GATA motifs ³	66.27%	*** 86.61%	59.51%
CpG islands ⁴	2.39%	3.67%	2.19%
SNPs ⁴	84.52%	** 89.42%	82.23%

Significance of difference in proportions between group A and B is denoted by * for each biological feature examined. ** denotes p-values between 5e-2 and 5e-3. *** denotes p-values < 5e-3. The p-values were obtained from the Fisher's Exact Test. The differential expressed genes in G1E and G1E-ER4 were obtained from the transcriptome data in G1E and G1E-ER4 cells¹ [15]. GATA1 binding peaks were obtained from [15]. GATA motifs³ were identified by MEME relevant tools [49]. Annotation data such as CpG islands⁴ and SNPs⁴ (dbSNP 128) were from database of UCSC genome browser [50].

ISSN: 1471-2164